I am trying to figure out how to make a hole smaller on a 3d printed .stl file. Any help would be appreciated.
I use Rhino3d to create STL’s. One of its commands is MeshtoNurbs. It allows you to go back to the polysurfaces with that command. I’d probably create the hole you want and then figure out how to add that to the existing file. I’d make a cylinder and split the object with it, then split the cylinder with the object, and finally delete the waste.
There are at least two ways. One is to fix it in CAD, the other in the slicer.
I typically use FreeCAD for this. Here’s my typical workflow:
- Import the STL
- Choose the Part workbench
- Part→Create shape from mesh
- Delete the mesh
- Select the shape and Part→Convert to solid
- Delete the shape, leaving only the solid
- Choose the Part Design workbench
- Select the solid, and create a new Body, which will use the shape as the base feature
- Fill in the hole
- Create a pocket or hole in the new feature with the size hole you actually want
It’s typically rather slow if the mesh has lots of “curves” in it; those will be represented by about ten bajillion triangles, all of which FreeCAD has to pay attention to.
I’ve ended up instead using the STL mesh as a model from which to re-model the part as an actual object, often making other useful changes at the same time.
Note that if the original source includes a STEP as well as STL file, the STEP will be much, much easier to work with. (In terms of 2d graphics, STL is to GIF or PNG as STEP is to PDF or SVG.)
I’m sure you can do this in other CAD as well; I just know FreeCAD which is free as in freedom as well as free as in beer. 
Some slicers let you add modifiers to the part on the bed and can also be used for this, but not necessarily with the same precision as doing it in CAD.
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